Alakazam

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

  1. Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
  2. Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
  3. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  4. Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.

Contact

If you need help or have any questions, please contact the Immcantation Group.

If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.

To receive alerts about Immcantation releases, news, events, and tutorials, join the Immcantation News Google Group. Membership settings can be adjusted to change the frequency of email updates.

Dependencies

Depends: ggplot2
Imports: airr, ape, dplyr, graphics, grid, igraph, Matrix, methods, progress, Rcpp, readr, rlang, scales, seqinr, stats, stringi, tibble, tidyr, utils, Biostrings, GenomicAlignments, IRanges
Suggests: cigarillo, knitr, rmarkdown, testthat

Authors

Susanna Marquez (cre, aut)
Namita Gupta (aut)
Nima Nouri (aut)
Ruoyi Jiang (aut)
Julian Zhou (aut)
Kenneth Hoehn (aut)
Daniel Gadala-Maria (ctb)
Edel Aron (ctb)
Cole Jensen (aut)
Gisela Gabernet (ctb)
Caroline Sullivan (ctb)
Hailong Meng (ctb)
Huimin Lyu (ctb)
Burhan Sabuwala (ctb)
Jason Vander Heiden (aut)
Steven Kleinstein (aut, cph)

Citing

To cite the alakazam package in publications, please use:

Gupta N, Vander Heiden J, Uduman M, Gadala-Maria D, Yaari G, Kleinstein S (2015). “Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.” Bioinformatics, 1-3. doi:10.1093/bioinformatics/btv359 https://doi.org/10.1093/bioinformatics/btv359.

To cite the Ig-specific lineage reconstruction and diversity methods, please use:

Stern J, Yaari G, Vander Heiden J, Church G, Donahue W, Hintzen R, Huttner A, Laman J, Nagra R, Nylander A, Pitt D, Ramanan S, Siddiqui B, Vigneault F, Kleinstein S, Hafler D, O’Connor K (2014). “B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.” Science Translational Medicine, 6(248), 248ra107. doi:10.1126/scitranslmed.3008879 https://doi.org/10.1126/scitranslmed.3008879.

License

AGPL-3